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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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Error: Could not connect to database: #25

Closed Knievl closed 4 years ago

Knievl commented 4 years ago

Hello,

as soon as i run tximeta, it is unable to connect to database, i tested the FTP url on my own and its perfectly fine. How can i solve this?

Best regards

 se <- tximeta(coldata)
 importing quantifications
 reading in files with read_tsv
 1 
 found matching transcriptome:
 [ Ensembl - Drosophila melanogaster - release 97 ]
 loading existing EnsDb created: 2020-01-18 13:16:29
 Error: Could not connect to database:
 unable to open database file
mikelove commented 4 years ago

It looks like there's a problem with your pre-existing EnsDb, that it got wiped out somehow or corrupted.

One thing you could do is to go into the BiocFileCache and remove this EnsDb entry so it will be downloaded again.

library(BiocFileCache)
bfc <- BiocFileCache()
bfcinfo(bfc)
bfcremove(bfc, rids="...")

Where you should fill in the rids that matches the EnsDb.

mikelove commented 4 years ago

I'm going to close this, but feel free to re-open if the above doesn't fix.